diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 4eb0d9ea963021227b0583fabf152eac649edf2b..759903efc6b9d089086d8c2f3ecc200f9daac22c 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -37,60 +37,6 @@ Local Distance Test scores (lDDT, DRMSD)
.. autoclass:: ost.mol.alg.lddt.CustomCompound
:members:
-.. function:: CheckStructure(ent, \
- bond_table, \
- angle_table, \
- nonbonded_table, \
- bond_tolerance, \
- angle_tolerance)
-
- Perform structural checks and filters the structure.
-
- :param ent: Structure to check
- :type ent: :class:`~ost.mol.EntityView`
- :param bond_table: List of bond stereo chemical parameters obtained from
- :class:`~ost.io.StereoChemicalParamsReader` or :func:`FillStereoChemicalParams`
- :type bond_table: :class:`~ost.mol.alg.StereoChemicalParams`
- :param angle_table: List of angle stereo chemical parameters obtained from
- :class:`~ost.io.StereoChemicalParamsReader` or :func:`FillStereoChemicalParams`
- :type angle_table: :class:`~ost.mol.alg.StereoChemicalParams`
- :param nonbonded_table: Information about the clashing distances obtained from
- :class:`~ost.io.StereoChemicalParamsReader` or :func:`FillClashingDistances`
- :type nonbonded_table: :class:`~ost.mol.alg.ClashingDistances`
- :param bond_tolerance: Tolerance in stddev for bonds
- :type bond_tolerance: :class:`float`
- :param angle_tolerance: Tolerance in stddev for angles
- :type angle_tolerance: :class:`float`
-
-
-.. class:: StereoChemicalProps(bond_table, angle_table, nonbonded_table)
-
- Object containing the stereo-chemical properties read form stereochmical_props.txt
- file.
-
- :param bond_table: Sets :attr:`bond_table`
- :param angle_table: Sets :attr:`angle_table`
- :param nonbonded_table: Sets :attr:`nonbonded_table`
-
- .. attribute:: bond_table
-
- Object containing bond parameters
-
- :type: :class:`~ost.mol.alg.StereoChemicalParams`
-
- .. attribute:: angle_table
-
- Object containing angle parameters
-
- :type: :class:`~ost.mol.alg.StereoChemicalParams`
-
- .. attribute:: nonbonded_table
-
- Object containing clashing distances parameters
-
- :type: :class:`~ost.mol.alg.ClashingDistances`
-
-
.. class:: lDDTSettings(radius=15, \
sequence_separation=0, \
cutoffs=(0.5, 1.0, 2.0, 4.0), \
@@ -137,6 +83,25 @@ Local Distance Test scores (lDDT, DRMSD)
:rtype: :class:`str`
+:mod:`stereochemistry <ost.mol.alg.stereochemistry>` -- Stereochemistry Checks
+--------------------------------------------------------------------------------
+
+.. warning::
+
+ Stereochemistry checks described in
+ `Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_ are
+ considered deprecated. They have been re-implemented and now support
+ nucleotides. The old code is still available and documented
+ :doc:`here <stereochemistry_deprecated>`.
+
+.. automodule:: ost.mol.alg.stereochemistry
+ :members:
+ :member-order: bysource
+ :synopsis: Stereochemistry checks
+
+.. currentmodule:: ost.mol.alg
+
+
:mod:`scoring <ost.mol.alg.scoring>` -- Specialized scoring functions
--------------------------------------------------------------------------------
diff --git a/modules/mol/alg/pymod/stereochemistry.py b/modules/mol/alg/pymod/stereochemistry.py
index 39713accdfdb3cdb35c483eaa1b79e81306bb48e..e3f43691f19f224b524664af863e886165936952 100644
--- a/modules/mol/alg/pymod/stereochemistry.py
+++ b/modules/mol/alg/pymod/stereochemistry.py
@@ -170,9 +170,9 @@ def GetBondParam(a1, a2, stereo_data):
""" Returns mean and standard deviation for bond
:param a1: First atom that defines bond
- :type a1: :class:`mol.AtomView`/:class:`mol.AtomHandle`
+ :type a1: :class:`ost.mol.AtomView`/:class:`ost.mol.AtomHandle`
:param a2: Second atom that defines bond
- :type a2: :class:`mol.AtomView`/:class:`mol.AtomHandle`
+ :type a2: :class:`ost.mol.AtomView`/:class:`ost.mol.AtomHandle`
:param stereo_data: Stereochemistry data
:type stereo_data: :class:`dict`
:returns: :class:`tuple` with mean and standard deviation. Values are None
@@ -201,11 +201,11 @@ def GetAngleParam(a1, a2, a3, stereo_data):
""" Returns mean and standard deviation for angle
:param a1: First atom that defines angle
- :type a1: :class:`mol.AtomView`/:class:`mol.AtomHandle`
+ :type a1: :class:`ost.mol.AtomView`/:class:`ost.mol.AtomHandle`
:param a2: Second atom that defines angle
- :type a2: :class:`mol.AtomView`/:class:`mol.AtomHandle`
- :param a3: Second atom that defines angle
- :type a3: :class:`mol.AtomView`/:class:`mol.AtomHandle`
+ :type a2: :class:`ost.mol.AtomView`/:class:`ost.mol.AtomHandle`
+ :param a3: Third atom that defines angle
+ :type a3: :class:`ost.mol.AtomView`/:class:`ost.mol.AtomHandle`
:param stereo_data: Stereochemistry data
:type stereo_data: :class:`dict`
:returns: :class:`tuple` with mean and standard deviation. Values are None
@@ -244,7 +244,7 @@ def GetClashes(ent, vdw_radii = None, tolerance = 1.5, disulfid_dist = 2.03,
The default values are not very sensitive.
:param ent: Entity for which you want to identify clashing atoms
- :type ent: :class:`EntityHandle`/:class:`EntityView`
+ :type ent: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
:param vdw_radii: Element based van der Waals radii. Only atoms of these
elements will be considered. If not given, default values
for all elements occuring in proteins/nucleotides are
@@ -259,7 +259,7 @@ def GetClashes(ent, vdw_radii = None, tolerance = 1.5, disulfid_dist = 2.03,
:param disulfid_tolerance: The respective tolerance
:type disulfid_dist: :class:`float`
:returns: A :class:`list` of pairs. Each pair consists of two
- :class:`mol.AtomView` from *ent* that are clashing.
+ :class:`ost.mol.AtomView` from *ent* that are clashing.
"""
if vdw_radii is None:
@@ -312,14 +312,14 @@ def GetBadBonds(ent, stereo_data = None, tolerance=12):
""" Identify unrealistic bonds
:param ent: Entity for which you want to identify unrealistic bonds
- :type ent: :class:`mol.EntityHandle`/:class:`mol.EntityView`
+ :type ent: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
:param stereo_data: Stereochemistry data
:type stereo_data: :class:`dict`
:param tolerance: Bonds that devaiate more than *tolerance* times standard
deviation from expected mean are considered bad
:type tolerance: :class:`int`
:returns: :class:`list` of pairs. Each pair consists of two
- :class:`mol.AtomHandle` from *ent* that represent bad bonds.
+ :class:`ost.mol.AtomHandle` from *ent* that represent bad bonds.
"""
assert("bond_data" in stereo_data)
@@ -339,14 +339,14 @@ def GetBadAngles(ent, stereo_data = None, tolerance=12):
""" Identify unrealistic angles
:param ent: Entity for which you want to identify unrealistic angles
- :type ent: :class:`mol.EntityHandle`/:class:`mol.EntityView`
+ :type ent: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
:param stereo_data: Stereochemistry data
:type stereo_data: :class:`dict`
:param tolerance: Angles that devaiate more than *tolerance* times standard
deviation from expected mean are considered bad
:type tolerance: :class:`int`
:returns: :class:`list` of tuples. Each tuple consists of three
- :class:`mol.AtomHandle` from *ent* that represent bad angles.
+ :class:`ost.mol.AtomHandle` from *ent* that represent bad angles.
"""
assert("angle_data" in stereo_data)
return_list = list()